The Round-Up #3

Vaccines, bacterial immune systems, sciency travel pictures, and more!

Welcome, or welcome back, to The Science Fictional Now! Today’s post is the latest in our Round-Up series, featuring a selection of the most interesting and informative things I’ve read recently. The first two of these were written on an ad hoc schedule, but I’m happy to announce that they’ll be published quarterly from now on.

This time around, we’ve got some cool new scientific papers, lots of vaccine news, and thought provoking articles on topics ranging from surrogacy to apocalyptic fiction. Stick around until the end for a few science- and nature-related pictures taken during my recent travels to England and Ireland. Enjoy!

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New scientific papers

We’ll start out with a few interesting scientific papers and preprints from the past few months. Note that there will probably be fewer of these in future Round-Ups since I’ll be shifting from biology to the history of science.

• The first AI-generated genomes: Brian Hie’s lab at the Arc Institute developed AI language models for generating new DNA sequences over the past year and a half, and now they’ve put them into practice. In a preprint published days before this Round-Up, they generated novel bacterial viruses (called bacteriophages or phages) that are highly infectious in E. coli. This is a bit of a full circle moment, as the virus they used as a template - called ΦX174 - was the first DNA genome ever sequenced, all the way back in 1977 by Fred Sanger’s lab. Niko McCarty wrote a popular article on the Hie Lab’s work for Asimov Press.

• Modular antiviral immune systems: Bacteria have been defending against phage infection for eons, which has inspired some extremely creative immune mechanisms. This has become a very hot field within molecular biology, in part because defense systems like CRISPR have shown promise for biotech. Some of my former colleagues in the Doudna Lab at UC Berkeley characterized another system called Hachiman last year, and they recently published a new preprint showing that Hachiman can fuse to other protein modules and still fight infection. This paper is a super interesting look at how these defense systems have evolved over time.

• RNA-guided transcription: Remarkably, some bacterial immune systems have even been co-opted for entirely new cellular functions. Sam Sternberg’s lab at Columbia described a fascinating example of this in a recent preprint, showing that CRISPR-Cas12f can join up with a protein called a sigma factor to transcribe DNA into RNA. Normally this requires an extra DNA motif called a promoter to tell the cell where to start reading DNA, but here the CRISPR guide RNA does that instead!

• An Egyptian with Mesopotamian ancestry: Researchers at the Crick Institute in London recently sequenced the genome of an Old Kingdom Egyptian man who lived more than 4500 years ago. The project was a collaboration between the labs of Pontus Skogland and Linus Girdland-Fink, and revealed that the man had ancestry from the Fertile Crescent in addition to Egypt.

• Effects of declining vaccination: Declining childhood vaccination rates in the US mean that diseases which today are afterthoughts could re-emerge in the future. A group of researchers from Stanford and Baylor modeled what could happen over the next few decades with lower rates of uptake for the measles-mumps-rubella (MMR) vaccine.

Vaccines

Dovetailing with the paper above…vaccines have been in the news a lot recently, and mostly for the wrong reasons. Accordingly, most of the articles below aren’t “interesting” in the enjoyable, thought-provoking sense - but they are full of important information that needs to be circulated widely.

• Florida’s natural experiment: Florida’s recent decision to remove all childhood vaccine mandates threw fuel into the flames of already declining vaccination. Brenda Goodman and Deidre Phillips wrote an article for CNN discussing the move’s potential consequences of the move, informed in part by the paper above.

• A new federal vaccine schedule?: Florida’s move came on the heels of an announcement that the federal government’s vaccine advisory panel would be reconsidering the CDC’s entire slate of recommended childhood vaccinations. Among other things, newly-appointed advisors have suggested the US should consider pared-down vaccination recommendations similar to those of Denmark. Katherine Wu penned a nice piece in The Atlantic on what happened and whether it actually makes sense for the US to implement such a schedule.

• State vaccine schedules: Preemptively responding to changes in federal vaccine schedules, Washington, Oregon, California, and Hawaii formed a consortium to create their own vaccine guidelines. Melody Gutierrez covered this for the LA Times; you can view the current recommendations here.

• COVID-19 vaccine efficacy: President Trump recently requested public efficacy data for the vaccines used during the pandemic, despite their utility already being well-documented. You can find nice summaries of the evidence in both a Bluesky thread from BK Titanji and a New York Times article from Carl Zimmer and Apoorva Mandavilli.

• mRNA contracts cancelled en masse: mRNA vaccines have been a particular target for HHS Secretary Robert F. Kennedy, Jr., who recently announced that over $500 million in mRNA vaccine funding would be retracted.¹ While RFK claimed that the decision was based on a lengthy science review, many physicians and vaccine experts disagreed with his agency’s findings. For reviews of the evidence, check out Jake Scott’s piece for STAT, and Beth Mole’s article for Ars Technica.

Biosecurity

• BWC verification: The Biological Weapons Convention turns 50 this year and has helped establish strong norms against bioweapons in that time. However, one of the convention’s major weaknesses has been its inability to systematically verify that member states are complying with its rules. A recent op-ed in the Bulletin of the Atomic Scientists made some thoughtful suggestions about how such a verification regime could be implemented and made politically feasible.

• Resilient AIxBio safeguards: As discussed in our last Round-Up, many biosecurity experts have become acutely worried about AI-enabled bioterrorism. The rapid pace of AI development means that creating effective safeguards will be an important and ongoing process. Richard Moulange wrote about this view in a recent Substack post.

• Bird and mammal flu testing: My friend Chris Pearson recently published a Substack post (his first!) about Australia’s bird testing program, which serves as a detection system for avian flu. He also discussed the idea of adding mammal testing to this regime. As someone who primarily thinks about US biosecurity, it was refreshing to read about a robust biosecurity system in another country.

• Nobody is running biosecurity for Trump: For all its strengths, US biosecurity has a massive management problem under the Trump administration. Anemone Franz and Britt Lampert published an op-ed in The Hill describing the federal government’s current lack of pandemic preparedness.

• Funding cuts hurt biosafety: Researchers who receive federal funding can be more effectively held to biosafety and biosecurity standards than those who don’t. In National Interest, Steph Batalis recently argued that pervasive research cuts erode the US government’s control over biosafety by partially forfeiting this key point of control.

Government and science

• Scientists’ resistance: Funding uncertainty and political encroachment on scientific freedom have plagued US scientists since the beginning of the year, and many have decided to push back, in particular through lawsuits and grant tracking. Dan Garisto, Max Kozlov, and Heidi Ledford described how scientists have used grant tracking, legal action, and other means to resist attacks on science in a news article for Nature.

• Political control over grantmaking: President Trump also passed an Executive Order last month requiring certain federal grants (including all for scientific research) to be approved by an appointee within the requisite agency. This effectively puts grants under political control, as they must now be deemed ideologically fit in order to be funded. John Timmer explained what this means in Ars Technica.

• NIH grants back on track: Surprisingly enough, though, the science funding crisis may be partially alleviated, as the NIH is finally on track to spend its budget for the year, report Megan Molteni, Anil Oza, and J. Emory Parker. Given everything else covered in this Round-Up however, it’s unlikely that this means science grantmaking is “back to normal” in the US.

Other

• Surrogacy suit: Reproductive biology has long been a hotbed for controversy, and the practice of surrogacy has provided no exception to that rule. The latest episode in the surrogacy saga took place when a venture capitalist sued her surrogate after a stillbirth. Emi Nietfeld wrote a truly hair-raising article about the affair for WIRED.

• Tad Friend recently published an essay about the longevity/anti-aging world for The New Yorker, centered on entrepreneur Peter Diamandis. The article is maybe less critical than its title would suggest, but very well-written and informative nonetheless. A good read if you’re looking to get an idea of what’s been going on in that field.

• CRISPR clinical trials in 2025: UC Berkeley’s Innovative Genomics Institute (my former employer) recently published their 2025 update on various CRISPR medicine’s clinical progress. The IGI’s Hope Henderson writes yearly updates, which are always highly detailed and informative.

• The real Illustrated Primer: Science fiction writer Neal Stephenson recently published a thoughtful essay on his Substack that serves as a nice conversation starter about AI in education. Stephenson’s take is especially relevant because he imagined a kind of AI tutor thirty years ago in his novel The Diamond Age.

• Leviathan and the zombie invasion: Bridger of the Library Ladder YouTube channel consistently puts out high-quality videos on science fiction, and his latest might be my favorite on the entire internet. It’s about the philosophical underpinnings of apocalyptic fiction, and shows how writers like Neal Stephenson, John Wyndham, and José Saramago are in conversation with philosophers like Thomas Hobbes and Jean-Paul Sartre - all without requiring you to leave the couch!

Travel photos

As promised!

A bust of Rosalind Franklin in the old library at Trinity College Dublin. Complete with a DNA-esque spiral motif, in the correct right-handed orientation.

Irish Women in STEM stamps that I picked up. Featuring astrophysicist Jocelyn Bell Burnell and geneticist Aoife McLysaght.

The Cliffs of Moher in County Clare, Ireland. The wind and rain were exhilarating, but cleared up long enough for me to snap a picture with slightly better lighting.

The “yeast room” at the Guinness Storehouse in Dublin.

Darwin’s Restaurant, also in Dublin. I’d wager they serve more biologists than the average spot in their neighborhood.

1. Specifically, contracts and grants for biotech and pharma companies made through the government agency BARDA.